Multiple sequence alignment - TraesCS7D01G517400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G517400 chr7D 100.000 4184 0 0 1 4184 616259179 616254996 0.000000e+00 7727.0
1 TraesCS7D01G517400 chr7D 91.430 1517 104 6 1581 3077 616219895 616221405 0.000000e+00 2058.0
2 TraesCS7D01G517400 chr7D 81.469 1457 226 23 1623 3077 616276402 616274988 0.000000e+00 1155.0
3 TraesCS7D01G517400 chr7D 80.639 1472 218 36 1620 3077 617027834 617029252 0.000000e+00 1077.0
4 TraesCS7D01G517400 chr7D 87.592 951 63 25 3094 4011 616221471 616222399 0.000000e+00 1051.0
5 TraesCS7D01G517400 chr7D 81.588 1184 201 13 1898 3077 616331549 616330379 0.000000e+00 963.0
6 TraesCS7D01G517400 chr7D 84.284 859 109 18 72 909 616218230 616219083 0.000000e+00 815.0
7 TraesCS7D01G517400 chr7D 89.169 674 32 12 934 1577 616219198 616219860 0.000000e+00 802.0
8 TraesCS7D01G517400 chr7D 83.498 303 31 9 450 733 224059326 224059024 8.920000e-67 265.0
9 TraesCS7D01G517400 chr7D 81.595 163 25 3 1155 1312 616276891 616276729 3.390000e-26 130.0
10 TraesCS7D01G517400 chr7D 75.248 303 57 9 1620 1904 617068462 617068764 1.220000e-25 128.0
11 TraesCS7D01G517400 chr7D 83.465 127 15 3 1155 1275 616333738 616333612 3.420000e-21 113.0
12 TraesCS7D01G517400 chr7D 79.856 139 23 4 3894 4028 616316303 616316166 3.440000e-16 97.1
13 TraesCS7D01G517400 chr7A 89.439 1515 131 8 1581 3077 709265719 709264216 0.000000e+00 1884.0
14 TraesCS7D01G517400 chr7A 83.032 1273 186 22 1812 3077 709285518 709284269 0.000000e+00 1127.0
15 TraesCS7D01G517400 chr7A 81.024 1465 212 40 1628 3077 709755314 709756727 0.000000e+00 1105.0
16 TraesCS7D01G517400 chr7A 86.260 1048 94 29 3105 4151 709264143 709263145 0.000000e+00 1092.0
17 TraesCS7D01G517400 chr7A 81.967 1098 146 36 408 1475 709266840 709265765 0.000000e+00 883.0
18 TraesCS7D01G517400 chr7A 76.949 885 179 22 1811 2682 709726173 709727045 8.140000e-132 481.0
19 TraesCS7D01G517400 chr7A 90.855 339 27 2 964 1302 709286253 709285919 6.380000e-123 451.0
20 TraesCS7D01G517400 chr7A 81.908 304 34 12 450 733 237515759 237516061 1.940000e-58 237.0
21 TraesCS7D01G517400 chr7A 85.976 164 18 5 1582 1745 709285704 709285546 2.000000e-38 171.0
22 TraesCS7D01G517400 chr7A 82.738 168 21 7 3102 3265 709284196 709284033 4.360000e-30 143.0
23 TraesCS7D01G517400 chr7A 81.529 157 12 11 1440 1580 709285892 709285737 3.420000e-21 113.0
24 TraesCS7D01G517400 chr7A 91.489 47 2 2 1535 1580 709265796 709265751 3.490000e-06 63.9
25 TraesCS7D01G517400 chr7B 81.340 1463 218 28 1623 3077 709591882 709590467 0.000000e+00 1138.0
26 TraesCS7D01G517400 chr7B 81.290 1240 187 21 1841 3077 709530394 709529197 0.000000e+00 963.0
27 TraesCS7D01G517400 chr7B 88.120 665 33 20 938 1577 709531289 709530646 0.000000e+00 749.0
28 TraesCS7D01G517400 chr7B 82.236 805 111 18 72 856 709517657 709516865 0.000000e+00 665.0
29 TraesCS7D01G517400 chr7B 79.536 992 158 24 2100 3077 711205584 711206544 0.000000e+00 665.0
30 TraesCS7D01G517400 chr7B 86.389 360 11 8 943 1292 709516847 709516516 3.980000e-95 359.0
31 TraesCS7D01G517400 chr7B 79.446 433 58 19 1324 1745 709515949 709515537 1.150000e-70 278.0
32 TraesCS7D01G517400 chr7B 83.168 303 32 5 450 733 173868719 173868417 4.150000e-65 259.0
33 TraesCS7D01G517400 chr7B 88.957 163 13 1 1583 1745 709530608 709530451 3.300000e-46 196.0
34 TraesCS7D01G517400 chr7B 84.337 166 20 6 3102 3264 709590394 709590232 1.560000e-34 158.0
35 TraesCS7D01G517400 chr7B 85.821 134 16 1 1155 1285 709592447 709592314 5.640000e-29 139.0
36 TraesCS7D01G517400 chr7B 83.465 127 14 3 248 369 709531962 709531838 1.230000e-20 111.0
37 TraesCS7D01G517400 chr1D 80.453 1458 199 44 1628 3077 408626009 408627388 0.000000e+00 1035.0
38 TraesCS7D01G517400 chr1D 83.750 160 19 4 1155 1309 408625455 408625612 1.210000e-30 145.0
39 TraesCS7D01G517400 chr1A 77.333 1275 242 36 1821 3077 583924633 583925878 0.000000e+00 710.0
40 TraesCS7D01G517400 chr4D 76.328 866 122 39 102 919 367950886 367950056 1.820000e-103 387.0
41 TraesCS7D01G517400 chr6B 77.131 739 102 42 137 831 76484064 76484779 2.380000e-97 366.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G517400 chr7D 616254996 616259179 4183 True 7727.000000 7727 100.000000 1 4184 1 chr7D.!!$R2 4183
1 TraesCS7D01G517400 chr7D 616218230 616222399 4169 False 1181.500000 2058 88.118750 72 4011 4 chr7D.!!$F3 3939
2 TraesCS7D01G517400 chr7D 617027834 617029252 1418 False 1077.000000 1077 80.639000 1620 3077 1 chr7D.!!$F1 1457
3 TraesCS7D01G517400 chr7D 616274988 616276891 1903 True 642.500000 1155 81.532000 1155 3077 2 chr7D.!!$R4 1922
4 TraesCS7D01G517400 chr7D 616330379 616333738 3359 True 538.000000 963 82.526500 1155 3077 2 chr7D.!!$R5 1922
5 TraesCS7D01G517400 chr7A 709755314 709756727 1413 False 1105.000000 1105 81.024000 1628 3077 1 chr7A.!!$F3 1449
6 TraesCS7D01G517400 chr7A 709263145 709266840 3695 True 980.725000 1884 87.288750 408 4151 4 chr7A.!!$R1 3743
7 TraesCS7D01G517400 chr7A 709726173 709727045 872 False 481.000000 481 76.949000 1811 2682 1 chr7A.!!$F2 871
8 TraesCS7D01G517400 chr7A 709284033 709286253 2220 True 401.000000 1127 84.826000 964 3265 5 chr7A.!!$R2 2301
9 TraesCS7D01G517400 chr7B 711205584 711206544 960 False 665.000000 665 79.536000 2100 3077 1 chr7B.!!$F1 977
10 TraesCS7D01G517400 chr7B 709529197 709531962 2765 True 504.750000 963 85.458000 248 3077 4 chr7B.!!$R3 2829
11 TraesCS7D01G517400 chr7B 709590232 709592447 2215 True 478.333333 1138 83.832667 1155 3264 3 chr7B.!!$R4 2109
12 TraesCS7D01G517400 chr7B 709515537 709517657 2120 True 434.000000 665 82.690333 72 1745 3 chr7B.!!$R2 1673
13 TraesCS7D01G517400 chr1D 408625455 408627388 1933 False 590.000000 1035 82.101500 1155 3077 2 chr1D.!!$F1 1922
14 TraesCS7D01G517400 chr1A 583924633 583925878 1245 False 710.000000 710 77.333000 1821 3077 1 chr1A.!!$F1 1256
15 TraesCS7D01G517400 chr4D 367950056 367950886 830 True 387.000000 387 76.328000 102 919 1 chr4D.!!$R1 817
16 TraesCS7D01G517400 chr6B 76484064 76484779 715 False 366.000000 366 77.131000 137 831 1 chr6B.!!$F1 694

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
404 424 0.460311 GGTCGACCCATCAGAATCGT 59.540 55.0 24.75 0.0 36.03 3.73 F
452 473 1.098869 TGGCACAACATTGACAACGT 58.901 45.0 0.00 0.0 31.92 3.99 F
872 1057 1.585297 ATTCGACCGGAACAAACGTT 58.415 45.0 9.46 0.0 37.50 3.99 F
1774 2762 0.652592 CACCGATGACAATTCCGCTC 59.347 55.0 0.00 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 2592 0.104304 AACCTCCTGTGACACGACAC 59.896 55.0 0.22 0.0 40.68 3.67 R
1617 2593 0.387929 GAACCTCCTGTGACACGACA 59.612 55.0 0.22 0.0 0.00 4.35 R
2760 5253 0.247736 AGTCCAATGTCTCCAGTCGC 59.752 55.0 0.00 0.0 0.00 5.19 R
3758 6351 0.037419 ATTCGTTGCAATGCCAACCC 60.037 50.0 14.04 0.0 41.50 4.11 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.559590 GATAAATTATCCTCATCCGGGAATG 57.440 40.000 0.00 0.00 36.37 2.67
25 26 5.582950 AAATTATCCTCATCCGGGAATGA 57.417 39.130 0.00 3.26 36.37 2.57
26 27 4.559862 ATTATCCTCATCCGGGAATGAC 57.440 45.455 0.00 0.00 36.37 3.06
27 28 1.059913 ATCCTCATCCGGGAATGACC 58.940 55.000 0.00 0.00 36.37 4.02
35 36 2.125269 GGGAATGACCGTCGGTGG 60.125 66.667 24.45 0.00 35.25 4.61
36 37 2.652095 GGGAATGACCGTCGGTGGA 61.652 63.158 24.45 8.56 35.25 4.02
37 38 1.520666 GGAATGACCGTCGGTGGAT 59.479 57.895 24.45 10.74 35.25 3.41
38 39 0.748450 GGAATGACCGTCGGTGGATA 59.252 55.000 24.45 5.66 35.25 2.59
39 40 1.137479 GGAATGACCGTCGGTGGATAA 59.863 52.381 24.45 2.08 35.25 1.75
40 41 2.419021 GGAATGACCGTCGGTGGATAAA 60.419 50.000 24.45 0.15 35.25 1.40
41 42 3.463944 GAATGACCGTCGGTGGATAAAT 58.536 45.455 24.45 2.69 35.25 1.40
42 43 3.553828 ATGACCGTCGGTGGATAAATT 57.446 42.857 24.45 0.00 35.25 1.82
43 44 4.675976 ATGACCGTCGGTGGATAAATTA 57.324 40.909 24.45 0.00 35.25 1.40
44 45 4.049546 TGACCGTCGGTGGATAAATTAG 57.950 45.455 24.45 0.00 35.25 1.73
45 46 2.798847 GACCGTCGGTGGATAAATTAGC 59.201 50.000 24.45 0.00 35.25 3.09
46 47 1.790623 CCGTCGGTGGATAAATTAGCG 59.209 52.381 2.08 0.00 36.73 4.26
47 48 1.191647 CGTCGGTGGATAAATTAGCGC 59.808 52.381 0.00 0.00 35.52 5.92
48 49 1.529865 GTCGGTGGATAAATTAGCGCC 59.470 52.381 2.29 0.00 35.52 6.53
49 50 1.139256 TCGGTGGATAAATTAGCGCCA 59.861 47.619 2.29 0.00 35.52 5.69
50 51 2.151202 CGGTGGATAAATTAGCGCCAT 58.849 47.619 2.29 0.00 0.00 4.40
51 52 2.159627 CGGTGGATAAATTAGCGCCATC 59.840 50.000 2.29 0.00 0.00 3.51
52 53 3.412386 GGTGGATAAATTAGCGCCATCT 58.588 45.455 2.29 0.00 0.00 2.90
53 54 4.575885 GGTGGATAAATTAGCGCCATCTA 58.424 43.478 2.29 0.00 0.00 1.98
54 55 4.392138 GGTGGATAAATTAGCGCCATCTAC 59.608 45.833 2.29 5.80 0.00 2.59
55 56 5.238583 GTGGATAAATTAGCGCCATCTACT 58.761 41.667 2.29 0.00 0.00 2.57
56 57 6.395629 GTGGATAAATTAGCGCCATCTACTA 58.604 40.000 2.29 0.00 0.00 1.82
57 58 6.531948 GTGGATAAATTAGCGCCATCTACTAG 59.468 42.308 2.29 0.00 0.00 2.57
58 59 6.436218 TGGATAAATTAGCGCCATCTACTAGA 59.564 38.462 2.29 0.00 0.00 2.43
59 60 6.975772 GGATAAATTAGCGCCATCTACTAGAG 59.024 42.308 2.29 0.00 0.00 2.43
60 61 7.148052 GGATAAATTAGCGCCATCTACTAGAGA 60.148 40.741 2.29 0.00 39.01 3.10
61 62 6.597832 AAATTAGCGCCATCTACTAGAGAT 57.402 37.500 2.29 0.00 46.52 2.75
79 80 8.001875 ACTAGAGATGCTCTAAAACAGATCCTA 58.998 37.037 0.00 0.00 41.74 2.94
82 83 9.373450 AGAGATGCTCTAAAACAGATCCTATAA 57.627 33.333 0.00 0.00 39.28 0.98
107 108 1.444836 CTCGTCCCGCAAAATAACCA 58.555 50.000 0.00 0.00 0.00 3.67
121 122 7.949428 CGCAAAATAACCATTGTTTTACATGAC 59.051 33.333 0.00 0.00 33.11 3.06
226 232 4.878397 CCATCCGCCATATTTCTAGGATTC 59.122 45.833 0.00 0.00 36.45 2.52
231 237 4.020218 CGCCATATTTCTAGGATTCCTCCA 60.020 45.833 8.94 0.00 44.79 3.86
244 250 5.492524 AGGATTCCTCCATCTTTTTACAGGA 59.507 40.000 0.00 0.00 44.79 3.86
288 303 1.646540 CAACCGCTTTCGTTCTGCA 59.353 52.632 0.00 0.00 0.00 4.41
290 305 0.814010 AACCGCTTTCGTTCTGCACT 60.814 50.000 0.00 0.00 0.00 4.40
337 352 0.756294 TCAACGTTGCTCCTTCCTCA 59.244 50.000 23.47 0.00 0.00 3.86
379 399 2.060980 AGAGCCTCCCACATCCGAC 61.061 63.158 0.00 0.00 0.00 4.79
404 424 0.460311 GGTCGACCCATCAGAATCGT 59.540 55.000 24.75 0.00 36.03 3.73
452 473 1.098869 TGGCACAACATTGACAACGT 58.901 45.000 0.00 0.00 31.92 3.99
458 480 4.596097 CACAACATTGACAACGTCATCAA 58.404 39.130 14.66 14.66 42.40 2.57
462 484 4.326826 ACATTGACAACGTCATCAAGGAT 58.673 39.130 24.54 11.80 42.40 3.24
468 500 3.007506 ACAACGTCATCAAGGATGTGGTA 59.992 43.478 6.15 0.00 38.80 3.25
702 755 4.758251 CACCTGCGGACGATGCCA 62.758 66.667 0.00 0.00 0.00 4.92
714 767 4.429522 ATGCCAGCGCCATGGACA 62.430 61.111 18.40 15.41 43.57 4.02
775 829 5.125739 TCGTTTTCAGGGTGTTTTGTGTTAT 59.874 36.000 0.00 0.00 0.00 1.89
776 830 5.457473 CGTTTTCAGGGTGTTTTGTGTTATC 59.543 40.000 0.00 0.00 0.00 1.75
784 841 6.837048 AGGGTGTTTTGTGTTATCTTTTAGGT 59.163 34.615 0.00 0.00 0.00 3.08
861 1046 7.042925 AAGATTTTTACGGAATCTATTCGACCG 60.043 37.037 6.81 6.81 41.66 4.79
862 1047 3.631145 TTACGGAATCTATTCGACCGG 57.369 47.619 12.27 0.00 46.45 5.28
869 1054 4.033702 GGAATCTATTCGACCGGAACAAAC 59.966 45.833 9.46 0.00 37.50 2.93
872 1057 1.585297 ATTCGACCGGAACAAACGTT 58.415 45.000 9.46 0.00 37.50 3.99
916 1101 8.594881 AAAAATGTTTTGCGGTATCATGTAAA 57.405 26.923 0.00 0.00 0.00 2.01
934 1216 3.356529 AAACCGATCTGCATTCCTCTT 57.643 42.857 0.00 0.00 0.00 2.85
935 1217 2.611225 ACCGATCTGCATTCCTCTTC 57.389 50.000 0.00 0.00 0.00 2.87
936 1218 2.114616 ACCGATCTGCATTCCTCTTCT 58.885 47.619 0.00 0.00 0.00 2.85
937 1219 2.503356 ACCGATCTGCATTCCTCTTCTT 59.497 45.455 0.00 0.00 0.00 2.52
938 1220 3.129871 CCGATCTGCATTCCTCTTCTTC 58.870 50.000 0.00 0.00 0.00 2.87
939 1221 3.181467 CCGATCTGCATTCCTCTTCTTCT 60.181 47.826 0.00 0.00 0.00 2.85
940 1222 4.440880 CGATCTGCATTCCTCTTCTTCTT 58.559 43.478 0.00 0.00 0.00 2.52
941 1223 4.270566 CGATCTGCATTCCTCTTCTTCTTG 59.729 45.833 0.00 0.00 0.00 3.02
1023 1315 4.144703 GGAGCCGGGGAAGACGAC 62.145 72.222 2.18 0.00 0.00 4.34
1303 1639 9.354673 TCCATTCCATTATTACTTCCTCAATTC 57.645 33.333 0.00 0.00 0.00 2.17
1435 2328 6.399743 TGCGTAATTGGTGAAACTATAGTGA 58.600 36.000 6.06 0.00 36.74 3.41
1478 2389 5.642491 TCTGCTCAGATTTCTTGTTCAGATG 59.358 40.000 0.00 0.00 31.41 2.90
1530 2464 4.652822 ACTAAACCCCTCTACAGCAAAAG 58.347 43.478 0.00 0.00 0.00 2.27
1577 2514 5.964958 TTTCTCCTTCAAAATACAGGCAG 57.035 39.130 0.00 0.00 0.00 4.85
1580 2517 6.121776 TCTCCTTCAAAATACAGGCAGTTA 57.878 37.500 0.00 0.00 0.00 2.24
1607 2583 5.703978 ATGCAACCCCTTTAAAAATTTGC 57.296 34.783 12.94 12.94 38.65 3.68
1614 2590 4.021456 CCCCTTTAAAAATTTGCGTCCTCT 60.021 41.667 0.00 0.00 0.00 3.69
1615 2591 5.161358 CCCTTTAAAAATTTGCGTCCTCTC 58.839 41.667 0.00 0.00 0.00 3.20
1616 2592 4.851558 CCTTTAAAAATTTGCGTCCTCTCG 59.148 41.667 0.00 0.00 0.00 4.04
1617 2593 5.427036 TTTAAAAATTTGCGTCCTCTCGT 57.573 34.783 0.00 0.00 0.00 4.18
1618 2594 2.969443 AAAATTTGCGTCCTCTCGTG 57.031 45.000 0.00 0.00 0.00 4.35
1659 2635 3.060602 GCCGGTTATAATCTCACTGCTC 58.939 50.000 1.90 0.00 0.00 4.26
1774 2762 0.652592 CACCGATGACAATTCCGCTC 59.347 55.000 0.00 0.00 0.00 5.03
1782 2770 1.936547 GACAATTCCGCTCATCAGGTC 59.063 52.381 0.00 0.00 0.00 3.85
1851 2839 3.848272 ATAACACGGGCAAAGTTCATG 57.152 42.857 0.00 0.00 0.00 3.07
1866 2854 7.308435 CAAAGTTCATGGAGACTGTAAATTCC 58.692 38.462 0.00 0.00 0.00 3.01
1952 4379 5.022122 AGAGGACTCTCATCATCTTGACAA 58.978 41.667 0.00 0.00 36.35 3.18
2165 4596 6.016777 ACAATACTCAGAAGGCTTGTTTTGAG 60.017 38.462 18.49 18.46 38.34 3.02
2237 4668 6.721668 TCAAGACTTGAGGACTTAGAGATCAA 59.278 38.462 13.99 0.00 34.08 2.57
2238 4669 7.233553 TCAAGACTTGAGGACTTAGAGATCAAA 59.766 37.037 13.99 0.00 34.08 2.69
2276 4707 4.565564 GGATGACTTAATCGTACCACACAC 59.434 45.833 0.00 0.00 0.00 3.82
2355 4795 3.790091 TCATGCTACTGATCTTGCTCAC 58.210 45.455 0.00 0.00 0.00 3.51
2378 4818 3.308438 TGAGTACAAAGGCCGAGTAAC 57.692 47.619 0.00 0.00 0.00 2.50
2402 4842 4.202441 CCTATAGTGCTTCATGGTTGCTT 58.798 43.478 0.00 0.00 0.00 3.91
2437 4883 1.039856 AACAATTGCGTTTGAGGCCT 58.960 45.000 3.86 3.86 0.00 5.19
2449 4896 3.543680 TTGAGGCCTCTAATGTACTGC 57.456 47.619 32.28 3.37 0.00 4.40
2525 4975 8.075574 TGTGCGAGCTTTTATATCAAAATATGG 58.924 33.333 0.00 0.00 30.59 2.74
2590 5057 5.741011 TCTTCAAACTTGGTGTTACTGTCT 58.259 37.500 0.00 0.00 38.03 3.41
2605 5072 9.419297 GTGTTACTGTCTGTGTCATCTTATTTA 57.581 33.333 0.00 0.00 0.00 1.40
2696 5163 8.774586 GCATATGACTTGTAAAATTATCGTCCT 58.225 33.333 6.97 0.00 0.00 3.85
2716 5189 6.578023 GTCCTTGCTAGAGATGTAAATGACT 58.422 40.000 0.00 0.00 0.00 3.41
2758 5251 3.871775 CATTGGTTGGACAGTGCAC 57.128 52.632 9.40 9.40 0.00 4.57
2759 5252 0.314935 CATTGGTTGGACAGTGCACC 59.685 55.000 14.63 0.00 0.00 5.01
2760 5253 1.172180 ATTGGTTGGACAGTGCACCG 61.172 55.000 14.63 5.70 0.00 4.94
2761 5254 3.660111 GGTTGGACAGTGCACCGC 61.660 66.667 14.63 2.66 0.00 5.68
2762 5255 4.012895 GTTGGACAGTGCACCGCG 62.013 66.667 14.63 0.00 0.00 6.46
2767 5260 4.969196 ACAGTGCACCGCGACTGG 62.969 66.667 24.13 10.59 39.81 4.00
2768 5261 4.662961 CAGTGCACCGCGACTGGA 62.663 66.667 14.63 0.00 35.61 3.86
2769 5262 4.363990 AGTGCACCGCGACTGGAG 62.364 66.667 14.63 0.00 0.00 3.86
2770 5263 4.357947 GTGCACCGCGACTGGAGA 62.358 66.667 8.23 0.00 0.00 3.71
2854 5355 8.862325 TCAAGAAAGAGCTGTATTTGGATTAA 57.138 30.769 0.00 0.00 0.00 1.40
2891 5392 2.734492 GCAAGCTTCCAATGCAGATGTC 60.734 50.000 0.00 0.00 39.81 3.06
2914 5415 1.738099 CTGAGGTCCGGTGCTTTCG 60.738 63.158 0.00 0.00 0.00 3.46
2916 5417 1.180456 TGAGGTCCGGTGCTTTCGTA 61.180 55.000 0.00 0.00 0.00 3.43
3067 5576 1.799403 CTGTTCTTGAGCAGCTGACAG 59.201 52.381 20.43 15.98 0.00 3.51
3073 5582 3.056962 TCTTGAGCAGCTGACAGTAGAAG 60.057 47.826 20.43 10.20 0.00 2.85
3097 5621 5.711506 GCAATATGGGGTGATGATGATTACA 59.288 40.000 0.00 0.00 0.00 2.41
3118 5678 1.442526 GCGGATCTGTGAATGGGCAG 61.443 60.000 2.89 0.00 0.00 4.85
3121 5681 1.476471 GGATCTGTGAATGGGCAGAGG 60.476 57.143 0.00 0.00 43.81 3.69
3201 5761 5.059404 AGTAAACCAATCCTTTTCGCATG 57.941 39.130 0.00 0.00 0.00 4.06
3205 5765 3.417101 ACCAATCCTTTTCGCATGTACA 58.583 40.909 0.00 0.00 0.00 2.90
3222 5782 6.414079 CATGTACACGCTGTCAATTAATCTC 58.586 40.000 0.00 0.00 0.00 2.75
3281 5842 3.301274 AGAATGCCCCTCTAGACTGTAC 58.699 50.000 0.00 0.00 0.00 2.90
3311 5872 6.549364 TGTTTTGGTGTCTACAAATGGAATCT 59.451 34.615 0.00 0.00 37.62 2.40
3312 5873 6.573664 TTTGGTGTCTACAAATGGAATCTG 57.426 37.500 0.00 0.00 33.26 2.90
3319 5892 4.721776 TCTACAAATGGAATCTGTAGGGCT 59.278 41.667 8.23 0.00 45.66 5.19
3399 5972 3.745975 TGTTCTGCCTTTTATGTGTCTCG 59.254 43.478 0.00 0.00 0.00 4.04
3407 5980 5.109210 CCTTTTATGTGTCTCGAGTGCATA 58.891 41.667 13.13 15.18 0.00 3.14
3477 6050 6.445786 TGTAAGAGGGTTATTTGTCCTGGTAT 59.554 38.462 0.00 0.00 0.00 2.73
3480 6053 6.896883 AGAGGGTTATTTGTCCTGGTATTAC 58.103 40.000 0.00 0.00 0.00 1.89
3483 6056 5.298527 GGGTTATTTGTCCTGGTATTACTGC 59.701 44.000 0.00 0.00 0.00 4.40
3504 6077 3.925913 GCAGCTACTGAAAGAACTCTGAG 59.074 47.826 2.45 2.45 37.43 3.35
3516 6089 4.446371 AGAACTCTGAGTGGTGAAAACTG 58.554 43.478 11.71 0.00 0.00 3.16
3575 6148 1.901591 TTTGCCAGCTCCTGAAAGAG 58.098 50.000 0.00 0.00 34.07 2.85
3591 6164 6.887545 CCTGAAAGAGGAAGTAAGACTCTCTA 59.112 42.308 0.00 0.00 46.33 2.43
3592 6165 7.067008 CCTGAAAGAGGAAGTAAGACTCTCTAG 59.933 44.444 0.00 0.00 46.33 2.43
3593 6166 6.887545 TGAAAGAGGAAGTAAGACTCTCTAGG 59.112 42.308 0.00 0.00 40.49 3.02
3594 6167 6.397217 AAGAGGAAGTAAGACTCTCTAGGT 57.603 41.667 0.00 0.00 40.49 3.08
3595 6168 6.397217 AGAGGAAGTAAGACTCTCTAGGTT 57.603 41.667 0.00 0.00 36.96 3.50
3597 6170 6.661805 AGAGGAAGTAAGACTCTCTAGGTTTG 59.338 42.308 0.00 0.00 36.96 2.93
3603 6176 1.153745 CTCTCTAGGTTTGCGCGCT 60.154 57.895 33.29 14.40 0.00 5.92
3608 6182 3.869473 TAGGTTTGCGCGCTTCGGT 62.869 57.895 33.29 16.28 38.94 4.69
3615 6189 2.074920 GCGCGCTTCGGTTGAAAAG 61.075 57.895 26.67 0.00 38.94 2.27
3642 6216 6.771188 AATATCTCTTCAAAATACCGAGCG 57.229 37.500 0.00 0.00 0.00 5.03
3661 6235 4.881920 AGCGTCTAAACAAAATTTGCCAT 58.118 34.783 5.52 0.00 0.00 4.40
3685 6259 1.512926 CATATTACTGCTCGGGTGGC 58.487 55.000 0.00 0.00 0.00 5.01
3689 6263 1.264749 TTACTGCTCGGGTGGCATCT 61.265 55.000 0.00 0.00 39.07 2.90
3703 6277 3.056536 GTGGCATCTGAGAGAACACACTA 60.057 47.826 7.89 0.00 31.86 2.74
3750 6343 2.070028 GAGGAACCTGAAGCGTTCTTC 58.930 52.381 0.00 8.67 46.85 2.87
3771 6364 3.988525 GTGCGGGTTGGCATTGCA 61.989 61.111 11.39 0.00 45.99 4.08
3778 6371 1.203523 GGGTTGGCATTGCAACGAATA 59.796 47.619 11.39 0.00 32.50 1.75
3782 6375 1.122849 GGCATTGCAACGAATATGCG 58.877 50.000 11.39 0.14 46.76 4.73
3794 6387 2.267426 GAATATGCGGTTTGTTTGGGC 58.733 47.619 0.00 0.00 0.00 5.36
3811 6404 2.109799 CGAATGCCATCCGAGCCT 59.890 61.111 0.00 0.00 0.00 4.58
3855 6448 2.225091 TGCTGAATGTTTGGGATCACCT 60.225 45.455 0.00 0.00 41.11 4.00
3856 6449 2.165030 GCTGAATGTTTGGGATCACCTG 59.835 50.000 0.00 0.00 41.11 4.00
3863 6456 0.404040 TTGGGATCACCTGGTTCACC 59.596 55.000 0.00 0.22 41.11 4.02
3864 6457 0.475632 TGGGATCACCTGGTTCACCT 60.476 55.000 0.00 0.00 41.11 4.00
3866 6459 0.108138 GGATCACCTGGTTCACCTCG 60.108 60.000 0.00 0.00 36.82 4.63
3870 6463 1.831286 ACCTGGTTCACCTCGTCGT 60.831 57.895 0.00 0.00 36.82 4.34
3875 6468 0.797249 GGTTCACCTCGTCGTCATCG 60.797 60.000 0.00 0.00 38.55 3.84
3890 6483 0.028505 CATCGCTTGAAAGATGGCCG 59.971 55.000 0.00 0.00 40.23 6.13
3912 6505 1.996187 GGAGGGGAAGGAGGGTGAC 60.996 68.421 0.00 0.00 0.00 3.67
3913 6506 2.284699 AGGGGAAGGAGGGTGACG 60.285 66.667 0.00 0.00 0.00 4.35
3915 6508 4.097361 GGGAAGGAGGGTGACGGC 62.097 72.222 0.00 0.00 0.00 5.68
3916 6509 3.319198 GGAAGGAGGGTGACGGCA 61.319 66.667 0.00 0.00 0.00 5.69
3917 6510 2.670148 GGAAGGAGGGTGACGGCAT 61.670 63.158 0.00 0.00 0.00 4.40
3918 6511 1.450312 GAAGGAGGGTGACGGCATG 60.450 63.158 0.00 0.00 0.00 4.06
3921 6514 4.101448 GAGGGTGACGGCATGCCT 62.101 66.667 33.07 20.54 0.00 4.75
3922 6515 4.415150 AGGGTGACGGCATGCCTG 62.415 66.667 33.07 26.84 0.00 4.85
3924 6517 4.722700 GGTGACGGCATGCCTGGT 62.723 66.667 33.07 24.58 0.00 4.00
3925 6518 2.672996 GTGACGGCATGCCTGGTT 60.673 61.111 33.07 15.37 0.00 3.67
3926 6519 2.672651 TGACGGCATGCCTGGTTG 60.673 61.111 33.07 19.95 0.00 3.77
3927 6520 2.672996 GACGGCATGCCTGGTTGT 60.673 61.111 33.07 23.08 0.00 3.32
3928 6521 2.672996 ACGGCATGCCTGGTTGTC 60.673 61.111 33.07 5.69 0.00 3.18
3929 6522 3.803082 CGGCATGCCTGGTTGTCG 61.803 66.667 33.07 14.34 34.37 4.35
3930 6523 4.120331 GGCATGCCTGGTTGTCGC 62.120 66.667 29.98 0.00 0.00 5.19
3931 6524 3.058160 GCATGCCTGGTTGTCGCT 61.058 61.111 6.36 0.00 0.00 4.93
3979 6572 4.778143 GGTGGGTAGGCGGCACTG 62.778 72.222 13.08 0.00 0.00 3.66
3991 6584 4.760047 GCACTGGTCGGTGGCGAT 62.760 66.667 11.38 0.00 37.65 4.58
4011 6604 1.913762 CCTCGTTCCCACTGGGTCT 60.914 63.158 14.25 0.00 44.74 3.85
4012 6605 1.592223 CTCGTTCCCACTGGGTCTC 59.408 63.158 14.25 5.16 44.74 3.36
4014 6607 2.663196 GTTCCCACTGGGTCTCGG 59.337 66.667 14.25 0.00 44.74 4.63
4015 6608 2.606519 TTCCCACTGGGTCTCGGG 60.607 66.667 14.25 0.00 44.74 5.14
4018 6611 4.087892 CCACTGGGTCTCGGGCTG 62.088 72.222 0.00 0.00 0.00 4.85
4019 6612 4.767255 CACTGGGTCTCGGGCTGC 62.767 72.222 0.00 0.00 0.00 5.25
4021 6614 4.463879 CTGGGTCTCGGGCTGCTG 62.464 72.222 0.00 0.00 0.00 4.41
4024 6617 4.459089 GGTCTCGGGCTGCTGGTC 62.459 72.222 0.00 0.00 0.00 4.02
4025 6618 3.695606 GTCTCGGGCTGCTGGTCA 61.696 66.667 0.00 0.00 0.00 4.02
4026 6619 3.695606 TCTCGGGCTGCTGGTCAC 61.696 66.667 0.00 0.00 0.00 3.67
4034 6627 1.560860 GCTGCTGGTCACGACAAGAC 61.561 60.000 5.73 0.00 34.21 3.01
4037 6630 0.582005 GCTGGTCACGACAAGACAAC 59.418 55.000 5.73 0.00 34.21 3.32
4044 6637 4.547532 GTCACGACAAGACAACAGTATCT 58.452 43.478 0.00 0.00 36.06 1.98
4065 6658 7.612668 ATCTGTATTAGCTCATGAATGATGC 57.387 36.000 0.00 0.00 36.02 3.91
4078 6671 3.242804 TGAATGATGCACATGCGTGTATG 60.243 43.478 12.10 1.29 46.92 2.39
4083 6676 1.273688 GCACATGCGTGTATGTCGTA 58.726 50.000 12.10 0.00 45.50 3.43
4086 6679 2.278875 CACATGCGTGTATGTCGTAGTG 59.721 50.000 12.10 0.00 39.17 2.74
4088 6681 2.993449 TGCGTGTATGTCGTAGTGAA 57.007 45.000 0.00 0.00 0.00 3.18
4110 6703 7.272084 GTGAAATTGCTGTAGCTAAATGAACTG 59.728 37.037 5.38 0.00 42.66 3.16
4114 6707 6.633500 TGCTGTAGCTAAATGAACTGTTTT 57.367 33.333 5.38 0.00 42.66 2.43
4131 6724 0.758123 TTTTGCAAGCCCAAGGGAAG 59.242 50.000 9.92 0.00 37.50 3.46
4138 6731 1.077429 GCCCAAGGGAAGCTACTGG 60.077 63.158 9.92 0.00 37.50 4.00
4152 6745 3.390135 GCTACTGGCGCTATTATGTTCA 58.610 45.455 7.64 0.00 0.00 3.18
4153 6746 3.430218 GCTACTGGCGCTATTATGTTCAG 59.570 47.826 7.64 5.07 0.00 3.02
4154 6747 3.543680 ACTGGCGCTATTATGTTCAGT 57.456 42.857 7.64 5.80 0.00 3.41
4155 6748 3.873910 ACTGGCGCTATTATGTTCAGTT 58.126 40.909 7.64 0.00 30.95 3.16
4156 6749 3.623060 ACTGGCGCTATTATGTTCAGTTG 59.377 43.478 7.64 0.00 30.95 3.16
4157 6750 3.867857 TGGCGCTATTATGTTCAGTTGA 58.132 40.909 7.64 0.00 0.00 3.18
4158 6751 3.871006 TGGCGCTATTATGTTCAGTTGAG 59.129 43.478 7.64 0.00 0.00 3.02
4159 6752 3.248602 GGCGCTATTATGTTCAGTTGAGG 59.751 47.826 7.64 0.00 0.00 3.86
4160 6753 3.303395 GCGCTATTATGTTCAGTTGAGGC 60.303 47.826 0.00 0.00 0.00 4.70
4161 6754 3.871006 CGCTATTATGTTCAGTTGAGGCA 59.129 43.478 0.00 0.00 0.00 4.75
4162 6755 4.260375 CGCTATTATGTTCAGTTGAGGCAC 60.260 45.833 0.00 0.00 0.00 5.01
4163 6756 4.035675 GCTATTATGTTCAGTTGAGGCACC 59.964 45.833 0.00 0.00 0.00 5.01
4164 6757 3.500448 TTATGTTCAGTTGAGGCACCA 57.500 42.857 0.00 0.00 0.00 4.17
4165 6758 2.363306 ATGTTCAGTTGAGGCACCAA 57.637 45.000 0.00 0.00 0.00 3.67
4166 6759 2.136298 TGTTCAGTTGAGGCACCAAA 57.864 45.000 0.00 0.00 0.00 3.28
4167 6760 2.451490 TGTTCAGTTGAGGCACCAAAA 58.549 42.857 0.00 0.00 0.00 2.44
4168 6761 3.030291 TGTTCAGTTGAGGCACCAAAAT 58.970 40.909 0.00 0.00 0.00 1.82
4169 6762 3.068024 TGTTCAGTTGAGGCACCAAAATC 59.932 43.478 0.00 0.00 0.00 2.17
4170 6763 2.942804 TCAGTTGAGGCACCAAAATCA 58.057 42.857 0.00 0.00 0.00 2.57
4171 6764 2.622942 TCAGTTGAGGCACCAAAATCAC 59.377 45.455 0.00 0.00 0.00 3.06
4172 6765 2.361757 CAGTTGAGGCACCAAAATCACA 59.638 45.455 0.00 0.00 0.00 3.58
4173 6766 2.624838 AGTTGAGGCACCAAAATCACAG 59.375 45.455 0.00 0.00 0.00 3.66
4174 6767 2.362077 GTTGAGGCACCAAAATCACAGT 59.638 45.455 0.00 0.00 0.00 3.55
4175 6768 3.500448 TGAGGCACCAAAATCACAGTA 57.500 42.857 0.00 0.00 0.00 2.74
4176 6769 4.032960 TGAGGCACCAAAATCACAGTAT 57.967 40.909 0.00 0.00 0.00 2.12
4177 6770 4.009675 TGAGGCACCAAAATCACAGTATC 58.990 43.478 0.00 0.00 0.00 2.24
4178 6771 4.263462 TGAGGCACCAAAATCACAGTATCT 60.263 41.667 0.00 0.00 0.00 1.98
4179 6772 5.045942 TGAGGCACCAAAATCACAGTATCTA 60.046 40.000 0.00 0.00 0.00 1.98
4180 6773 6.006275 AGGCACCAAAATCACAGTATCTAT 57.994 37.500 0.00 0.00 0.00 1.98
4181 6774 7.136822 AGGCACCAAAATCACAGTATCTATA 57.863 36.000 0.00 0.00 0.00 1.31
4182 6775 7.573710 AGGCACCAAAATCACAGTATCTATAA 58.426 34.615 0.00 0.00 0.00 0.98
4183 6776 7.499232 AGGCACCAAAATCACAGTATCTATAAC 59.501 37.037 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.281100 GTCATTCCCGGATGAGGATAATTTATC 59.719 40.741 0.73 7.73 36.76 1.75
1 2 7.112779 GTCATTCCCGGATGAGGATAATTTAT 58.887 38.462 0.73 0.00 36.76 1.40
2 3 6.472887 GTCATTCCCGGATGAGGATAATTTA 58.527 40.000 0.73 0.00 36.76 1.40
3 4 5.316987 GTCATTCCCGGATGAGGATAATTT 58.683 41.667 0.73 0.00 36.76 1.82
4 5 4.263506 GGTCATTCCCGGATGAGGATAATT 60.264 45.833 0.73 0.00 36.76 1.40
5 6 3.264450 GGTCATTCCCGGATGAGGATAAT 59.736 47.826 0.73 0.00 36.76 1.28
6 7 2.637872 GGTCATTCCCGGATGAGGATAA 59.362 50.000 0.73 0.00 36.76 1.75
7 8 2.257207 GGTCATTCCCGGATGAGGATA 58.743 52.381 0.73 0.00 36.76 2.59
8 9 1.059913 GGTCATTCCCGGATGAGGAT 58.940 55.000 0.73 0.00 36.76 3.24
9 10 1.399744 CGGTCATTCCCGGATGAGGA 61.400 60.000 0.73 0.00 44.32 3.71
10 11 1.069765 CGGTCATTCCCGGATGAGG 59.930 63.158 0.73 0.00 44.32 3.86
11 12 4.758692 CGGTCATTCCCGGATGAG 57.241 61.111 0.73 0.00 44.32 2.90
18 19 1.968050 ATCCACCGACGGTCATTCCC 61.968 60.000 18.72 0.00 31.02 3.97
19 20 0.748450 TATCCACCGACGGTCATTCC 59.252 55.000 18.72 0.00 31.02 3.01
20 21 2.589798 TTATCCACCGACGGTCATTC 57.410 50.000 18.72 0.00 31.02 2.67
21 22 3.553828 ATTTATCCACCGACGGTCATT 57.446 42.857 18.72 6.96 31.02 2.57
22 23 3.553828 AATTTATCCACCGACGGTCAT 57.446 42.857 18.72 14.49 31.02 3.06
23 24 3.738899 GCTAATTTATCCACCGACGGTCA 60.739 47.826 18.72 7.16 31.02 4.02
24 25 2.798847 GCTAATTTATCCACCGACGGTC 59.201 50.000 18.72 0.00 31.02 4.79
25 26 2.800629 CGCTAATTTATCCACCGACGGT 60.801 50.000 15.37 15.37 35.62 4.83
26 27 1.790623 CGCTAATTTATCCACCGACGG 59.209 52.381 13.61 13.61 0.00 4.79
27 28 1.191647 GCGCTAATTTATCCACCGACG 59.808 52.381 0.00 0.00 0.00 5.12
28 29 1.529865 GGCGCTAATTTATCCACCGAC 59.470 52.381 7.64 0.00 0.00 4.79
29 30 1.139256 TGGCGCTAATTTATCCACCGA 59.861 47.619 7.64 0.00 0.00 4.69
30 31 1.588674 TGGCGCTAATTTATCCACCG 58.411 50.000 7.64 0.00 0.00 4.94
31 32 3.412386 AGATGGCGCTAATTTATCCACC 58.588 45.455 7.64 0.00 0.00 4.61
32 33 5.238583 AGTAGATGGCGCTAATTTATCCAC 58.761 41.667 7.64 0.00 0.00 4.02
33 34 5.483685 AGTAGATGGCGCTAATTTATCCA 57.516 39.130 7.64 0.00 0.00 3.41
34 35 6.864342 TCTAGTAGATGGCGCTAATTTATCC 58.136 40.000 7.64 0.00 0.00 2.59
35 36 7.763356 TCTCTAGTAGATGGCGCTAATTTATC 58.237 38.462 7.64 0.00 0.00 1.75
36 37 7.704578 TCTCTAGTAGATGGCGCTAATTTAT 57.295 36.000 7.64 0.00 0.00 1.40
37 38 7.704578 ATCTCTAGTAGATGGCGCTAATTTA 57.295 36.000 7.64 0.00 43.62 1.40
38 39 6.597832 ATCTCTAGTAGATGGCGCTAATTT 57.402 37.500 7.64 0.00 43.62 1.82
60 61 9.429359 CGATTTATAGGATCTGTTTTAGAGCAT 57.571 33.333 0.00 0.00 43.62 3.79
61 62 7.385205 GCGATTTATAGGATCTGTTTTAGAGCA 59.615 37.037 0.00 0.00 43.62 4.26
62 63 7.148557 GGCGATTTATAGGATCTGTTTTAGAGC 60.149 40.741 0.00 0.00 41.11 4.09
63 64 8.091449 AGGCGATTTATAGGATCTGTTTTAGAG 58.909 37.037 0.00 0.00 39.20 2.43
64 65 7.963532 AGGCGATTTATAGGATCTGTTTTAGA 58.036 34.615 0.00 0.00 40.37 2.10
65 66 7.062371 CGAGGCGATTTATAGGATCTGTTTTAG 59.938 40.741 0.00 0.00 0.00 1.85
66 67 6.866770 CGAGGCGATTTATAGGATCTGTTTTA 59.133 38.462 0.00 0.00 0.00 1.52
67 68 5.696724 CGAGGCGATTTATAGGATCTGTTTT 59.303 40.000 0.00 0.00 0.00 2.43
68 69 5.221461 ACGAGGCGATTTATAGGATCTGTTT 60.221 40.000 0.00 0.00 0.00 2.83
69 70 4.281182 ACGAGGCGATTTATAGGATCTGTT 59.719 41.667 0.00 0.00 0.00 3.16
70 71 3.827302 ACGAGGCGATTTATAGGATCTGT 59.173 43.478 0.00 0.00 0.00 3.41
107 108 6.723298 TTTGTCCTGGTCATGTAAAACAAT 57.277 33.333 0.00 0.00 0.00 2.71
140 142 1.816572 GCCGTTTTACAGGACCTGGTT 60.817 52.381 25.34 8.13 35.51 3.67
226 232 4.265073 CAGGTCCTGTAAAAAGATGGAGG 58.735 47.826 11.09 0.00 0.00 4.30
231 237 5.098663 TCCTACCAGGTCCTGTAAAAAGAT 58.901 41.667 17.85 0.00 36.53 2.40
244 250 4.807643 GCTGAAATTTCACTCCTACCAGGT 60.808 45.833 16.91 0.00 33.19 4.00
288 303 1.376037 GCTTAGTGGCAGCGGAAGT 60.376 57.895 0.00 0.00 0.00 3.01
290 305 1.079127 GAGCTTAGTGGCAGCGGAA 60.079 57.895 0.00 0.00 42.55 4.30
321 336 1.004440 GCTGAGGAAGGAGCAACGT 60.004 57.895 0.00 0.00 35.15 3.99
359 379 2.191641 GGATGTGGGAGGCTCTGC 59.808 66.667 15.23 5.58 0.00 4.26
379 399 3.537874 GATGGGTCGACCTCGGGG 61.538 72.222 32.52 0.00 41.11 5.73
394 414 1.071385 GGAGATGCCCACGATTCTGAT 59.929 52.381 0.00 0.00 0.00 2.90
404 424 4.113815 CCGCCTTGGAGATGCCCA 62.114 66.667 0.00 0.00 42.00 5.36
429 450 3.257393 GTTGTCAATGTTGTGCCAAACA 58.743 40.909 4.01 4.01 43.82 2.83
443 464 3.498018 CACATCCTTGATGACGTTGTCAA 59.502 43.478 10.84 13.62 45.96 3.18
448 469 2.859165 ACCACATCCTTGATGACGTT 57.141 45.000 10.84 0.00 42.09 3.99
452 473 1.831106 ACGCTACCACATCCTTGATGA 59.169 47.619 10.84 0.00 42.09 2.92
458 480 2.367202 CCCCACGCTACCACATCCT 61.367 63.158 0.00 0.00 0.00 3.24
462 484 2.118732 TCTCCCCACGCTACCACA 59.881 61.111 0.00 0.00 0.00 4.17
468 500 4.680537 ACCTCGTCTCCCCACGCT 62.681 66.667 0.00 0.00 39.74 5.07
501 534 1.841556 AAGGAACCTGACCGCCTCA 60.842 57.895 0.00 0.00 0.00 3.86
576 609 2.202557 CATCTCGTACACGGCGCA 60.203 61.111 10.83 0.00 40.29 6.09
642 675 0.260230 TCGAAGAGATCCTGGAGGCT 59.740 55.000 1.52 1.73 34.44 4.58
673 706 3.663176 CAGGTGTGGCGTGCTTGG 61.663 66.667 0.00 0.00 0.00 3.61
702 755 1.968017 CTGTGTTGTCCATGGCGCT 60.968 57.895 6.96 0.00 0.00 5.92
714 767 2.631062 TGGGTTCATACTCGTCTGTGTT 59.369 45.455 0.00 0.00 0.00 3.32
752 806 3.224884 ACACAAAACACCCTGAAAACG 57.775 42.857 0.00 0.00 0.00 3.60
807 864 4.702131 GTCAGATGTAGAGCCCATTTGTTT 59.298 41.667 0.00 0.00 0.00 2.83
808 865 4.263462 TGTCAGATGTAGAGCCCATTTGTT 60.263 41.667 0.00 0.00 0.00 2.83
844 901 1.683943 TCCGGTCGAATAGATTCCGT 58.316 50.000 0.00 0.00 36.95 4.69
857 1042 7.985634 TTATAGTATAACGTTTGTTCCGGTC 57.014 36.000 5.91 0.00 39.54 4.79
894 1079 6.096695 GGTTTACATGATACCGCAAAACATT 58.903 36.000 0.00 0.00 0.00 2.71
897 1082 4.092816 CGGTTTACATGATACCGCAAAAC 58.907 43.478 19.28 8.26 46.86 2.43
909 1094 3.879295 AGGAATGCAGATCGGTTTACATG 59.121 43.478 0.00 0.00 0.00 3.21
910 1095 4.130118 GAGGAATGCAGATCGGTTTACAT 58.870 43.478 0.00 0.00 0.00 2.29
911 1096 3.197766 AGAGGAATGCAGATCGGTTTACA 59.802 43.478 0.00 0.00 0.00 2.41
913 1098 4.162320 AGAAGAGGAATGCAGATCGGTTTA 59.838 41.667 0.00 0.00 0.00 2.01
914 1099 3.054802 AGAAGAGGAATGCAGATCGGTTT 60.055 43.478 0.00 0.00 0.00 3.27
916 1101 2.114616 AGAAGAGGAATGCAGATCGGT 58.885 47.619 0.00 0.00 0.00 4.69
919 1200 5.064962 CACAAGAAGAAGAGGAATGCAGATC 59.935 44.000 0.00 0.00 0.00 2.75
922 1203 4.070716 ACACAAGAAGAAGAGGAATGCAG 58.929 43.478 0.00 0.00 0.00 4.41
934 1216 9.537192 TCGACTTTTCTTTTATACACAAGAAGA 57.463 29.630 0.00 0.00 39.58 2.87
937 1219 9.321562 ACTTCGACTTTTCTTTTATACACAAGA 57.678 29.630 0.00 0.00 0.00 3.02
938 1220 9.370126 CACTTCGACTTTTCTTTTATACACAAG 57.630 33.333 0.00 0.00 0.00 3.16
939 1221 9.100554 TCACTTCGACTTTTCTTTTATACACAA 57.899 29.630 0.00 0.00 0.00 3.33
940 1222 8.651391 TCACTTCGACTTTTCTTTTATACACA 57.349 30.769 0.00 0.00 0.00 3.72
941 1223 9.582223 CTTCACTTCGACTTTTCTTTTATACAC 57.418 33.333 0.00 0.00 0.00 2.90
951 1233 3.804873 AGCTCACTTCACTTCGACTTTTC 59.195 43.478 0.00 0.00 0.00 2.29
1208 1526 1.447838 CATGGTGGTTCTCCGACCG 60.448 63.158 0.00 0.00 42.83 4.79
1352 2220 1.794116 CAGCAAATCCCGCAAAACAAG 59.206 47.619 0.00 0.00 0.00 3.16
1353 2221 1.863267 CAGCAAATCCCGCAAAACAA 58.137 45.000 0.00 0.00 0.00 2.83
1478 2389 7.042254 ACTGTAACTAAAAATGACGGTTCAGAC 60.042 37.037 0.00 0.00 34.35 3.51
1538 2473 3.715495 AGAAATACGAGCAGATGCAGAG 58.285 45.455 7.68 0.41 45.16 3.35
1605 2581 2.976350 ACGACACGAGAGGACGCA 60.976 61.111 0.00 0.00 36.70 5.24
1606 2582 2.502080 CACGACACGAGAGGACGC 60.502 66.667 0.00 0.00 36.70 5.19
1607 2583 1.154450 GACACGACACGAGAGGACG 60.154 63.158 0.00 0.00 39.31 4.79
1614 2590 1.652563 CTCCTGTGACACGACACGA 59.347 57.895 0.22 0.00 42.86 4.35
1615 2591 1.371758 CCTCCTGTGACACGACACG 60.372 63.158 0.22 0.00 42.86 4.49
1616 2592 0.104304 AACCTCCTGTGACACGACAC 59.896 55.000 0.22 0.00 40.68 3.67
1617 2593 0.387929 GAACCTCCTGTGACACGACA 59.612 55.000 0.22 0.00 0.00 4.35
1618 2594 0.387929 TGAACCTCCTGTGACACGAC 59.612 55.000 0.22 0.00 0.00 4.34
1659 2635 1.672356 CACGGCCTCTTTCAGTGGG 60.672 63.158 0.00 0.00 29.86 4.61
1774 2762 1.100510 CCAGTGCCATTGACCTGATG 58.899 55.000 0.00 0.00 0.00 3.07
1782 2770 0.390603 CATTGGTGCCAGTGCCATTG 60.391 55.000 0.82 0.00 36.33 2.82
1851 2839 7.461918 GTTGAATAACGGAATTTACAGTCTCC 58.538 38.462 0.00 0.00 0.00 3.71
1877 2865 4.640771 TTGATTCCTATCCCACTATGCC 57.359 45.455 0.00 0.00 0.00 4.40
1999 4426 6.127869 ACTCGGTAATCAGATATCTTCCGATG 60.128 42.308 21.61 18.63 43.45 3.84
2003 4430 6.982852 TCAACTCGGTAATCAGATATCTTCC 58.017 40.000 1.33 0.72 0.00 3.46
2012 4439 4.499183 AGCTTCTTCAACTCGGTAATCAG 58.501 43.478 0.00 0.00 0.00 2.90
2021 4448 1.349357 AGTGGGGAGCTTCTTCAACTC 59.651 52.381 0.00 0.00 0.00 3.01
2165 4596 7.565323 AAATCTCCAAATATCTGAACAGAGC 57.435 36.000 10.26 0.00 41.33 4.09
2237 4668 2.108075 TCATCCACACCAGAACACCATT 59.892 45.455 0.00 0.00 0.00 3.16
2238 4669 1.704628 TCATCCACACCAGAACACCAT 59.295 47.619 0.00 0.00 0.00 3.55
2276 4707 6.303970 CAGCAAATGTTGAAGTTTATCGAGTG 59.696 38.462 0.00 0.00 0.00 3.51
2370 4810 2.595238 AGCACTATAGGGGTTACTCGG 58.405 52.381 0.00 0.00 0.00 4.63
2378 4818 3.480470 CAACCATGAAGCACTATAGGGG 58.520 50.000 3.68 0.00 0.00 4.79
2437 4883 2.638480 GCATGGGGCAGTACATTAGA 57.362 50.000 0.00 0.00 43.97 2.10
2449 4896 4.101274 TGGAATTACATTGAATGCATGGGG 59.899 41.667 4.84 0.00 0.00 4.96
2605 5072 4.927049 AGGGACTGAAACATGACATGAAT 58.073 39.130 22.19 9.68 37.18 2.57
2716 5189 5.437060 GGCCAGTTGAAGAACTCCATTATA 58.563 41.667 0.00 0.00 40.68 0.98
2751 5244 4.662961 TCCAGTCGCGGTGCACTG 62.663 66.667 21.79 21.79 37.40 3.66
2753 5246 4.357947 TCTCCAGTCGCGGTGCAC 62.358 66.667 8.80 8.80 0.00 4.57
2754 5247 4.357947 GTCTCCAGTCGCGGTGCA 62.358 66.667 6.13 0.00 0.00 4.57
2755 5248 3.649277 ATGTCTCCAGTCGCGGTGC 62.649 63.158 6.13 0.00 0.00 5.01
2756 5249 1.079819 AATGTCTCCAGTCGCGGTG 60.080 57.895 6.13 4.06 0.00 4.94
2758 5251 1.811266 CCAATGTCTCCAGTCGCGG 60.811 63.158 6.13 0.00 0.00 6.46
2759 5252 1.078759 GTCCAATGTCTCCAGTCGCG 61.079 60.000 0.00 0.00 0.00 5.87
2760 5253 0.247736 AGTCCAATGTCTCCAGTCGC 59.752 55.000 0.00 0.00 0.00 5.19
2761 5254 2.341257 CAAGTCCAATGTCTCCAGTCG 58.659 52.381 0.00 0.00 0.00 4.18
2762 5255 2.079925 GCAAGTCCAATGTCTCCAGTC 58.920 52.381 0.00 0.00 0.00 3.51
2767 5260 3.076621 TCACATGCAAGTCCAATGTCTC 58.923 45.455 0.00 0.00 0.00 3.36
2768 5261 3.079578 CTCACATGCAAGTCCAATGTCT 58.920 45.455 0.00 0.00 0.00 3.41
2769 5262 2.816087 ACTCACATGCAAGTCCAATGTC 59.184 45.455 0.00 0.00 0.00 3.06
2770 5263 2.867624 ACTCACATGCAAGTCCAATGT 58.132 42.857 0.00 0.00 0.00 2.71
2839 5340 8.770438 TTTGGTCAAATTAATCCAAATACAGC 57.230 30.769 12.68 0.00 42.53 4.40
2854 5355 4.901868 AGCTTGCAATCATTTGGTCAAAT 58.098 34.783 0.00 3.34 41.33 2.32
2934 5435 0.543749 GCATACAGGGAGCTTCCACT 59.456 55.000 15.31 0.00 38.64 4.00
2936 5437 1.264749 ACGCATACAGGGAGCTTCCA 61.265 55.000 15.31 0.00 38.64 3.53
2942 5443 2.279517 GGCGACGCATACAGGGAG 60.280 66.667 23.09 0.00 0.00 4.30
3067 5576 4.973168 TCATCACCCCATATTGCTTCTAC 58.027 43.478 0.00 0.00 0.00 2.59
3073 5582 5.711506 TGTAATCATCATCACCCCATATTGC 59.288 40.000 0.00 0.00 0.00 3.56
3097 5621 1.528824 CCCATTCACAGATCCGCCT 59.471 57.895 0.00 0.00 0.00 5.52
3118 5678 0.108756 AAGCGCTTCGAGGTTACCTC 60.109 55.000 18.98 20.76 46.44 3.85
3121 5681 0.442699 CCAAAGCGCTTCGAGGTTAC 59.557 55.000 25.24 0.00 0.00 2.50
3201 5761 4.561606 ACGAGATTAATTGACAGCGTGTAC 59.438 41.667 0.00 0.00 0.00 2.90
3205 5765 3.585862 ACACGAGATTAATTGACAGCGT 58.414 40.909 0.00 0.00 0.00 5.07
3271 5832 5.692204 CACCAAAACAGTCAGTACAGTCTAG 59.308 44.000 0.00 0.00 0.00 2.43
3281 5842 5.811399 TTTGTAGACACCAAAACAGTCAG 57.189 39.130 0.00 0.00 34.80 3.51
3423 5996 3.270877 ACAAGGCATAATGAGGACGAAC 58.729 45.455 0.00 0.00 0.00 3.95
3425 5998 3.627395 AACAAGGCATAATGAGGACGA 57.373 42.857 0.00 0.00 0.00 4.20
3426 5999 3.689161 TGAAACAAGGCATAATGAGGACG 59.311 43.478 0.00 0.00 0.00 4.79
3427 6000 5.402398 GTTGAAACAAGGCATAATGAGGAC 58.598 41.667 0.00 0.00 0.00 3.85
3436 6009 4.469657 TCTTACAGGTTGAAACAAGGCAT 58.530 39.130 0.00 0.00 0.00 4.40
3477 6050 5.011125 AGAGTTCTTTCAGTAGCTGCAGTAA 59.989 40.000 16.64 0.15 0.00 2.24
3480 6053 3.679025 CAGAGTTCTTTCAGTAGCTGCAG 59.321 47.826 10.11 10.11 0.00 4.41
3483 6056 4.922692 CACTCAGAGTTCTTTCAGTAGCTG 59.077 45.833 0.00 0.00 0.00 4.24
3504 6077 7.876896 TTAAGTTTGTTTCAGTTTTCACCAC 57.123 32.000 0.00 0.00 0.00 4.16
3541 6114 4.795635 GCTGGCAAATGTGTACATGAACAA 60.796 41.667 0.00 0.00 36.56 2.83
3575 6148 5.412640 GCAAACCTAGAGAGTCTTACTTCC 58.587 45.833 0.00 0.00 0.00 3.46
3592 6165 4.322385 AACCGAAGCGCGCAAACC 62.322 61.111 35.10 17.18 39.11 3.27
3593 6166 2.975167 TTCAACCGAAGCGCGCAAAC 62.975 55.000 35.10 21.54 39.11 2.93
3594 6167 2.324332 TTTCAACCGAAGCGCGCAAA 62.324 50.000 35.10 18.93 39.11 3.68
3595 6168 2.324332 TTTTCAACCGAAGCGCGCAA 62.324 50.000 35.10 13.41 39.11 4.85
3597 6170 2.051703 TTTTCAACCGAAGCGCGC 60.052 55.556 26.66 26.66 39.11 6.86
3603 6176 8.842358 AAGAGATATTACACTTTTCAACCGAA 57.158 30.769 0.00 0.00 0.00 4.30
3615 6189 8.488764 GCTCGGTATTTTGAAGAGATATTACAC 58.511 37.037 0.00 0.00 0.00 2.90
3637 6211 3.360758 GGCAAATTTTGTTTAGACGCTCG 59.639 43.478 10.65 0.00 0.00 5.03
3667 6241 1.128200 TGCCACCCGAGCAGTAATAT 58.872 50.000 0.00 0.00 34.69 1.28
3670 6244 1.220749 GATGCCACCCGAGCAGTAA 59.779 57.895 0.00 0.00 44.90 2.24
3685 6259 4.686839 TCGTAGTGTGTTCTCTCAGATG 57.313 45.455 0.00 0.00 0.00 2.90
3689 6263 3.382227 TGGTTTCGTAGTGTGTTCTCTCA 59.618 43.478 0.00 0.00 0.00 3.27
3703 6277 2.268076 GGCAGTGGCATGGTTTCGT 61.268 57.895 12.58 0.00 43.71 3.85
3758 6351 0.037419 ATTCGTTGCAATGCCAACCC 60.037 50.000 14.04 0.00 41.50 4.11
3765 6358 2.473530 ACCGCATATTCGTTGCAATG 57.526 45.000 12.66 12.66 40.14 2.82
3768 6361 1.537638 ACAAACCGCATATTCGTTGCA 59.462 42.857 0.00 0.00 40.14 4.08
3771 6364 3.570559 CCAAACAAACCGCATATTCGTT 58.429 40.909 0.00 0.00 0.00 3.85
3778 6371 1.739338 TTCGCCCAAACAAACCGCAT 61.739 50.000 0.00 0.00 0.00 4.73
3782 6375 2.527671 GCATTCGCCCAAACAAACC 58.472 52.632 0.00 0.00 0.00 3.27
3794 6387 2.109799 AGGCTCGGATGGCATTCG 59.890 61.111 22.12 22.12 34.73 3.34
3830 6423 5.055812 GTGATCCCAAACATTCAGCAAAAA 58.944 37.500 0.00 0.00 0.00 1.94
3855 6448 0.242825 GATGACGACGAGGTGAACCA 59.757 55.000 0.00 0.00 38.89 3.67
3856 6449 0.797249 CGATGACGACGAGGTGAACC 60.797 60.000 0.00 0.00 42.66 3.62
3863 6456 1.318785 CTTTCAAGCGATGACGACGAG 59.681 52.381 0.00 0.00 42.66 4.18
3864 6457 1.068816 TCTTTCAAGCGATGACGACGA 60.069 47.619 0.00 0.00 42.66 4.20
3866 6459 2.029728 CCATCTTTCAAGCGATGACGAC 59.970 50.000 0.00 0.00 39.43 4.34
3870 6463 1.382522 GGCCATCTTTCAAGCGATGA 58.617 50.000 0.00 0.00 39.43 2.92
3875 6468 0.449388 CTCACGGCCATCTTTCAAGC 59.551 55.000 2.24 0.00 0.00 4.01
3890 6483 1.690985 CCCTCCTTCCCCTCCTCAC 60.691 68.421 0.00 0.00 0.00 3.51
3898 6491 4.097361 GCCGTCACCCTCCTTCCC 62.097 72.222 0.00 0.00 0.00 3.97
3912 6505 3.803082 CGACAACCAGGCATGCCG 61.803 66.667 30.50 23.56 41.95 5.69
3913 6506 4.120331 GCGACAACCAGGCATGCC 62.120 66.667 30.12 30.12 0.00 4.40
3915 6508 2.693762 CCAGCGACAACCAGGCATG 61.694 63.158 0.00 0.00 0.00 4.06
3916 6509 2.202236 ATCCAGCGACAACCAGGCAT 62.202 55.000 0.00 0.00 0.00 4.40
3917 6510 2.803155 GATCCAGCGACAACCAGGCA 62.803 60.000 0.00 0.00 0.00 4.75
3918 6511 2.045926 ATCCAGCGACAACCAGGC 60.046 61.111 0.00 0.00 0.00 4.85
3920 6513 1.364626 GCAGATCCAGCGACAACCAG 61.365 60.000 0.00 0.00 0.00 4.00
3921 6514 1.375908 GCAGATCCAGCGACAACCA 60.376 57.895 0.00 0.00 0.00 3.67
3922 6515 3.490890 GCAGATCCAGCGACAACC 58.509 61.111 0.00 0.00 0.00 3.77
3930 6523 4.559063 CTGGGGGCGCAGATCCAG 62.559 72.222 10.83 15.72 40.46 3.86
4014 6607 2.280797 TTGTCGTGACCAGCAGCC 60.281 61.111 0.00 0.00 0.00 4.85
4015 6608 1.300931 TCTTGTCGTGACCAGCAGC 60.301 57.895 0.00 0.00 0.00 5.25
4016 6609 0.249447 TGTCTTGTCGTGACCAGCAG 60.249 55.000 0.00 0.00 33.83 4.24
4017 6610 0.176910 TTGTCTTGTCGTGACCAGCA 59.823 50.000 0.00 0.00 33.83 4.41
4018 6611 0.582005 GTTGTCTTGTCGTGACCAGC 59.418 55.000 0.00 0.00 33.83 4.85
4019 6612 1.860950 CTGTTGTCTTGTCGTGACCAG 59.139 52.381 0.00 0.00 33.83 4.00
4020 6613 1.206132 ACTGTTGTCTTGTCGTGACCA 59.794 47.619 0.00 0.00 33.83 4.02
4021 6614 1.935933 ACTGTTGTCTTGTCGTGACC 58.064 50.000 0.00 0.00 33.83 4.02
4022 6615 4.383052 CAGATACTGTTGTCTTGTCGTGAC 59.617 45.833 0.00 0.00 35.21 3.67
4023 6616 4.037565 ACAGATACTGTTGTCTTGTCGTGA 59.962 41.667 0.00 0.00 42.59 4.35
4024 6617 4.299155 ACAGATACTGTTGTCTTGTCGTG 58.701 43.478 0.00 0.00 42.59 4.35
4025 6618 4.585955 ACAGATACTGTTGTCTTGTCGT 57.414 40.909 0.00 0.00 42.59 4.34
4026 6619 7.043986 GCTAATACAGATACTGTTGTCTTGTCG 60.044 40.741 9.63 0.00 42.59 4.35
4034 6627 8.877808 TTCATGAGCTAATACAGATACTGTTG 57.122 34.615 9.63 0.00 42.59 3.33
4037 6630 9.872721 ATCATTCATGAGCTAATACAGATACTG 57.127 33.333 0.00 0.00 40.64 2.74
4044 6637 6.056884 TGTGCATCATTCATGAGCTAATACA 58.943 36.000 5.60 0.00 40.64 2.29
4078 6671 3.927142 AGCTACAGCAATTTCACTACGAC 59.073 43.478 3.70 0.00 45.16 4.34
4083 6676 7.175641 AGTTCATTTAGCTACAGCAATTTCACT 59.824 33.333 3.70 0.00 45.16 3.41
4086 6679 7.308435 ACAGTTCATTTAGCTACAGCAATTTC 58.692 34.615 3.70 0.00 45.16 2.17
4088 6681 6.824305 ACAGTTCATTTAGCTACAGCAATT 57.176 33.333 3.70 0.00 45.16 2.32
4110 6703 0.467804 TCCCTTGGGCTTGCAAAAAC 59.532 50.000 0.00 0.00 0.00 2.43
4114 6707 2.209315 GCTTCCCTTGGGCTTGCAA 61.209 57.895 0.00 0.00 0.00 4.08
4131 6724 3.390135 TGAACATAATAGCGCCAGTAGC 58.610 45.455 2.29 0.00 38.52 3.58
4138 6731 3.303395 GCCTCAACTGAACATAATAGCGC 60.303 47.826 0.00 0.00 0.00 5.92
4144 6737 3.500448 TGGTGCCTCAACTGAACATAA 57.500 42.857 0.00 0.00 0.00 1.90
4145 6738 3.500448 TTGGTGCCTCAACTGAACATA 57.500 42.857 0.00 0.00 0.00 2.29
4151 6744 2.361757 TGTGATTTTGGTGCCTCAACTG 59.638 45.455 0.00 0.00 0.00 3.16
4152 6745 2.624838 CTGTGATTTTGGTGCCTCAACT 59.375 45.455 0.00 0.00 0.00 3.16
4153 6746 2.362077 ACTGTGATTTTGGTGCCTCAAC 59.638 45.455 0.00 0.00 0.00 3.18
4154 6747 2.665165 ACTGTGATTTTGGTGCCTCAA 58.335 42.857 0.00 0.00 0.00 3.02
4155 6748 2.363306 ACTGTGATTTTGGTGCCTCA 57.637 45.000 0.00 0.00 0.00 3.86
4156 6749 4.265073 AGATACTGTGATTTTGGTGCCTC 58.735 43.478 0.00 0.00 0.00 4.70
4157 6750 4.307032 AGATACTGTGATTTTGGTGCCT 57.693 40.909 0.00 0.00 0.00 4.75
4158 6751 7.639945 GTTATAGATACTGTGATTTTGGTGCC 58.360 38.462 0.00 0.00 0.00 5.01


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.